DiffBind
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see DiffBind.
Differential Binding Analysis of ChIP-Seq Peak Data
Bioconductor version: 3.16
Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.
Author: Rory Stark [aut, cre], Gord Brown [aut]
Maintainer: Rory Stark <rory.stark at cruk.cam.ac.uk>
citation("DiffBind")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DiffBind")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DiffBind")| DiffBind: Differential binding analysis of ChIP-Seq peak data | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, BiomedicalInformatics, CellBiology, ChIPSeq, DNaseSeq, DifferentialMethylation, DifferentialPeakCalling, Epigenetics, FunctionalGenomics, GeneRegulation, HistoneModification, MethylSeq, MultipleComparison, Normalization, PeakDetection, RIPSeq, ReportWriting, Sequencing, Software |
| Version | 3.8.4 |
| In Bioconductor since | BioC 2.9 (R-2.14) (12.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0), GenomicRanges, SummarizedExperiment |
| Imports | RColorBrewer, amap, gplots, grDevices, limma, GenomicAlignments, locfit, stats, utils, IRanges, lattice, systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel, parallel, S4Vectors, Rsamtools(>= 2.13.1), DESeq2, methods, graphics, ggrepel, apeglm, ashr, GreyListChIP |
| System Requirements | GNU make |
| URL | https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/DiffBind |
See More
| Suggests | BiocStyle, testthat, xtable |
| Linking To | Rhtslib(>= 1.99.1), Rcpp |
| Enhances | rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb, profileplyr, rtracklayer, grid |
| Depends On Me | ChIPQC, vulcan |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DiffBind_3.8.4.tar.gz |
| Windows Binary | DiffBind_3.8.4.zip (64-bit only) |
| macOS Binary (x86_64) | DiffBind_3.8.4.tgz |
| macOS Binary (arm64) | DiffBind_3.8.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DiffBind |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DiffBind |
| Bioc Package Browser | https://code.bioconductor.org/browse/DiffBind/ |
| Package Short Url | https://bioconductor.org/packages/DiffBind/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.16 | Source Archive |